Workflow

This workflow performs differential expression analysis on single- or paired-end RNA-seq data. After adapter removal with Cutadapt, reads were mapped and gene counts were generated with STAR. Gene counts of replicated were summed up. Integrated normalization and differential expression analysis was conducted with DESeq2 following standard procedure as outlined in the manual.

Detailed software versions can be found under Rules.

Results

MDS

hg38_PE_all_count_edegR_plot_MDS.png Download

Multidimensional scaling (MDS) analysis over the normalized counts of all genes.

hg38_PE_fraction_count_edegR_plot_MDS.png Download

Multidimensional scaling (MDS) analysis over the normalized counts of all genes.

hg38_PE_salmonAlignment_estcount_edegR_plot_MDS.png Download

Multidimensional scaling (MDS) analysis over the normalized counts of all genes.

hg38_PE_salmonReads_estcount_edegR_plot_MDS.png Download

Multidimensional scaling (MDS) analysis over the normalized counts of all genes.

hg38_PE_unique_count_edegR_plot_MDS.png Download

Multidimensional scaling (MDS) analysis over the normalized counts of all genes.

PCA

hg38_PE_all_count_edegR_plot_PCA.png Download

Principal component analysis over the normalized counts of all genes.

hg38_PE_fraction_count_edegR_plot_PCA.png Download

Principal component analysis over the normalized counts of all genes.

hg38_PE_salmonAlignment_estcount_edegR_plot_PCA.png Download

Principal component analysis over the normalized counts of all genes.

hg38_PE_salmonReads_estcount_edegR_plot_PCA.png Download

Principal component analysis over the normalized counts of all genes.

hg38_PE_unique_count_edegR_plot_PCA.png Download

Principal component analysis over the normalized counts of all genes.

Pie biotype

hg38_PE_all_count_edegR_plot_biotype.png Download

Pie chart of summarized counts for each biotype-class to detect if data is contaminated

hg38_PE_fraction_count_edegR_plot_biotype.png Download

Pie chart of summarized counts for each biotype-class to detect if data is contaminated

hg38_PE_salmonAlignment_estcount_edegR_plot_biotype.png Download

Pie chart of summarized counts for each biotype-class to detect if data is contaminated

hg38_PE_salmonReads_estcount_edegR_plot_biotype.png Download

Pie chart of summarized counts for each biotype-class to detect if data is contaminated

hg38_PE_unique_count_edegR_plot_biotype.png Download

Pie chart of summarized counts for each biotype-class to detect if data is contaminated

Quality control

multiqc.html Download

Quality controls aggregated into an interactive report via MultiQC.

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Rules

Rule Jobs Output Singularity Conda environment
install_R_package 1
  • viper_0.0.0.9000.txt
  • r-venndiagram=1.6.20
  • bioconductor-annotate=1.58.0=r351_0
  • bioconductor-annotationdbi=1.42.1=r351_0
  • bioconductor-biobase=2.40.0=r351h470a237_0
  • bioconductor-biocgenerics=0.26.0=r351_0
  • bioconductor-biocparallel=1.14.2=r351h26a2512_0
  • bioconductor-biomart=2.36.1=r351_0
  • bioconductor-biostrings=2.48.0=r351h470a237_0
  • bioconductor-bsgenome=1.48.0=r351_0
  • bioconductor-delayedarray=0.6.6=r351_0
  • bioconductor-deseq=1.32.0=r351h470a237_0
  • bioconductor-deseq2=1.20.0=r351hfc679d8_0
  • bioconductor-easyrnaseq=2.16.0=r351_0
  • bioconductor-edger=3.22.5=r351hfc679d8_0
  • bioconductor-genefilter=1.62.0=r351h26a2512_0
  • bioconductor-geneplotter=1.58.0=r351_0
  • bioconductor-genomeinfodb=1.16.0=r351_0
  • bioconductor-genomeinfodbdata=1.1.0=r351_0
  • bioconductor-genomeintervals=1.36.0=r351_0
  • bioconductor-genomicalignments=1.16.0=r351h470a237_0
  • bioconductor-genomicfeatures=1.32.3=r351_0
  • bioconductor-genomicranges=1.32.7=r351h470a237_0
  • bioconductor-iranges=2.14.12=r351h470a237_0
  • bioconductor-limma=3.36.5=r351h470a237_0
  • bioconductor-rsamtools=1.32.3=r351hfc679d8_0
  • bioconductor-rtracklayer=1.40.6=r351h470a237_0
  • bioconductor-s4vectors=0.18.3=r351h470a237_0
  • bioconductor-shortread=1.38.0=r351hfc679d8_0
  • bioconductor-summarizedexperiment=1.10.1=r351_0
  • bioconductor-tximport=1.8.0=r351_0
  • bioconductor-xvector=0.20.0=r351h470a237_0
  • bioconductor-zlibbioc=1.26.0=r351h470a237_0
  • r-data.table=1.11.6=r351hc070d10_0
  • bzip2=1.0.6=h470a237_2
  • ca-certificates=2018.11.29=ha4d7672_0
  • cairo=1.14.12=h276e583_5
  • curl=7.61.0=h93b3f91_2
  • fontconfig=2.13.1=h65d0f4c_0
  • freetype=2.9.1=h6debe1e_4
  • gettext=0.19.8.1=h5e8e0c9_1
  • glib=2.56.2=h464dc38_1
  • gmp=6.1.2=hfc679d8_0
  • graphite2=1.3.12=hfc679d8_1
  • harfbuzz=1.9.0=h04dbb29_1
  • icu=58.2=hfc679d8_0
  • jpeg=9c=h470a237_1
  • krb5=1.14.6=0
  • lapack=3.6.1=1
  • libffi=3.2.1=hfc679d8_5
  • libgfortran=3.0.0=1
  • libiconv=1.15=h470a237_3
  • libpng=1.6.36=ha92aebf_0
  • libssh2=1.8.0=h5b517e9_3
  • libstdcxx-ng=7.2.0=hdf63c60_3
  • libtiff=4.0.10=he6b73bb_0
  • libuuid=2.32.1=h470a237_2
  • libxcb=1.13=h470a237_2
  • libxml2=2.9.8=h422b904_5
  • ncurses=6.1=hfc679d8_1
  • openblas=0.2.20=8
  • openssl=1.0.2p=h470a237_1
  • pandoc=2.5=0
  • pango=1.40.14=he752989_2
  • pcre=8.41=hfc679d8_3
  • pixman=0.34.0=h470a237_3
  • pthread-stubs=0.4=h470a237_1
  • r-acepack=1.4.1=r351h364d78e_2
  • r-assertthat=0.2.0=r351h6115d3f_1001
  • r-backports=1.1.2=r351hc070d10_1
  • r-base=3.5.1=h4fe35fd_1
  • r-base64enc=0.1_3=r351hc070d10_2
  • r-bh=1.66.0_1=r351_2001
  • r-bindr=0.1.1=r351h6115d3f_1001
  • r-bindrcpp=0.2.2=r351h9d2a408_1
  • r-bit=1.1_12=r351h470a237_2
  • r-bit64=0.9_7=r351hc070d10_0
  • r-bitops=1.0_6=r351hc070d10_2
  • r-blob=1.1.1=r351_1001
  • r-broom=0.5.0=r351h6115d3f_1002
  • r-callr=3.0.0=r351h6115d3f_1000
  • r-catools=1.17.1.1=r351h9d2a408_2
  • r-cellranger=1.1.0=r351h6115d3f_1001
  • r-checkmate=1.8.5=r351hc070d10_2
  • r-cli=1.0.0=r351h6115d3f_1001
  • r-clipr=0.4.1=r351h6115d3f_1001
  • r-cluster=2.0.7_1=r351h364d78e_0
  • r-codetools=0.2_15=r351h6115d3f_1001
  • r-colorspace=1.3_2=r351hc070d10_2
  • r-cowplot=0.9.3=r351h6115d3f_1001
  • r-crayon=1.3.4=r351h6115d3f_1001
  • r-curl=3.2=r351hc070d10_2
  • r-dbi=1.0.0=r351h6115d3f_1001
  • r-dbplyr=1.2.2=r351h6115d3f_1001
  • r-digest=0.6.18=r351hc070d10_0
  • r-dplyr=0.7.6=r351h9d2a408_1
  • r-evaluate=0.11=r351h6115d3f_1000
  • r-fansi=0.3.0=r351hc070d10_0
  • r-fitdistrplus=1.0_11=r351h6115d3f_1000
  • r-forcats=0.3.0=r351h6115d3f_1001
  • r-foreign=0.8_71=r351hc070d10_2
  • r-formatr=1.5=r351h6115d3f_1001
  • r-formula=1.2_3=r351h6115d3f_1001
  • r-furrr=0.1.0=r351h6115d3f_1000
  • r-futile.logger=1.4.3=r351h6115d3f_1001
  • r-futile.options=1.0.1=r351h6115d3f_1000
  • r-future=1.10.0=r351h6115d3f_1000
  • r-gdata=2.18.0=r351h6115d3f_1001
  • r-ggplot2=3.1.0=r351h6115d3f_1000
  • r-globals=0.12.2=r351h6115d3f_1000
  • r-glue=1.3.0=r351h470a237_2
  • r-gplots=3.0.1=r351h6115d3f_1001
  • r-gridextra=2.3=r351h6115d3f_1001
  • r-gtable=0.2.0=r351h6115d3f_1001
  • r-gtools=3.8.1=r351hc070d10_2
  • r-haven=1.1.2=r351h9d2a408_2
  • r-highr=0.7=r351h6115d3f_1001
  • r-hmisc=4.1_1=r351h364d78e_1
  • r-hms=0.4.2=r351h6115d3f_1000
  • r-htmltable=1.12=r351h6115d3f_1000
  • r-htmltools=0.3.6=r351hfc679d8_2
  • r-htmlwidgets=1.2=r351h6115d3f_1000
  • r-httr=1.3.1=r351h6115d3f_1001
  • r-hwriter=1.3.2=r351h6115d3f_1001
  • r-intervals=0.15.1=r351h9d2a408_2
  • r-jsonlite=1.5=r351hc070d10_2
  • r-kernsmooth=2.23_15=r351h364d78e_2
  • r-knitr=1.20=r351h6115d3f_1001
  • r-labeling=0.3=r351h6115d3f_1001
  • r-lambda.r=1.2.3=r351h6115d3f_1000
  • r-lattice=0.20_35=r351hc070d10_0
  • r-latticeextra=0.6_28=r351h6115d3f_1001
  • r-lazyeval=0.2.1=r351hc070d10_2
  • r-listenv=0.7.0=r351h6115d3f_1001
  • r-lmtest=0.9_36=r351h364d78e_0
  • r-locfit=1.5_9.1=r351h470a237_2
  • r-lsd=3.0=r351_1001
  • r-lsei=1.2_0=r351ha44fe06_2
  • r-lubridate=1.7.4=r351h9d2a408_1
  • r-magrittr=1.5=r351h6115d3f_1001
  • r-markdown=0.8=r351hc070d10_3
  • r-mass=7.3_50=r351hc070d10_2
  • r-matrix=1.2_14=r351hc070d10_2
  • r-matrixstats=0.54.0=r351hc070d10_0
  • r-memoise=1.1.0=r351h6115d3f_1001
  • r-mgcv=1.8_24=r351hc070d10_2
  • r-mime=0.5=r351hc070d10_2
  • r-modelr=0.1.2=r351h6115d3f_1001
  • r-munsell=0.5.0=r351h6115d3f_1001
  • r-nlme=3.1_137=r351h364d78e_0
  • r-nnet=7.3_12=r351hc070d10_2
  • r-npsurv=0.4_0=r351h6115d3f_1000
  • r-openssl=1.0.2=r351h9f97512_0
  • r-pillar=1.3.0=r351h6115d3f_1000
  • r-pkgconfig=2.0.2=r351h6115d3f_1001
  • r-plogr=0.2.0=r351h6115d3f_1001
  • r-plyr=1.8.4=r351h9d2a408_2
  • r-prettyunits=1.0.2=r351h6115d3f_1001
  • r-processx=3.2.0=r351hc070d10_1
  • r-progress=1.2.0=r351h6115d3f_1002
  • r-ps=1.1.0=r351hc070d10_1
  • r-purrr=0.2.5=r351hc070d10_2
  • r-r6=2.2.2=r351h6115d3f_1001
  • r-rcolorbrewer=1.1_2=r351h6115d3f_1001
  • r-rcpp=1.0.0=r351h9d2a408_0
  • r-rcpparmadillo=0.9.100.5.0=r351h9d2a408_0
  • r-rcurl=1.95_4.11=r351h86b9717_2
  • r-readr=1.1.1=r351h9d2a408_2
  • r-readxl=1.1.0=r351h9d2a408_2
  • r-rematch=1.0.1=r351h6115d3f_1001
  • r-reprex=0.2.0=r351h6115d3f_1001
  • r-reshape2=1.4.3=r351h9d2a408_2
  • r-rlang=0.3.0.1=r351h470a237_0
  • r-rmarkdown=1.10=r351h6115d3f_1001
  • r-rpart=4.1_13=r351hc070d10_2
  • r-rprojroot=1.3_2=r351h6115d3f_1001
  • r-rsqlite=2.1.1=r351h9d2a408_0
  • r-rstudioapi=0.7=r351h6115d3f_1001
  • r-rvest=0.3.2=r351h6115d3f_1001
  • r-scales=1.0.0=r351h9d2a408_1
  • r-selectr=0.4_1=r351h6115d3f_1000
  • r-snow=0.4_3=r351h6115d3f_1000
  • r-stringi=1.2.4=r351h9d2a408_1
  • r-stringr=1.3.1=r351h6115d3f_1001
  • r-survival=2.42_6=r351hc070d10_1
  • r-tibble=1.4.2=r351hc070d10_2
  • r-tidyr=0.8.1=r351h9d2a408_2
  • r-tidyselect=0.2.4=r351h9d2a408_3
  • r-tidyverse=1.2.1=r351h6115d3f_1001
  • r-tinytex=0.8=r351h6115d3f_1000
  • r-utf8=1.1.4=r351hc070d10_0
  • r-vcd=1.4_4=r351h6115d3f_1001
  • r-viridis=0.5.1=r351h6115d3f_1001
  • r-viridislite=0.3.0=r351h6115d3f_1001
  • r-whisker=0.3_2=r351h6115d3f_1001
  • r-withr=2.1.2=r351h6115d3f_1000
  • r-xfun=0.3=r351h6115d3f_1001
  • r-xml=3.98_1.16=r351hc070d10_0
  • r-xml2=1.2.0=r351h9d2a408_2
  • r-xtable=1.8_3=r351_2000
  • r-yaml=2.2.0=r351hc070d10_1
  • r-zoo=1.8_3=r351hc070d10_0
  • readline=7.0=haf1bffa_1
  • tk=8.6.9=ha92aebf_0
  • xorg-kbproto=1.0.7=h470a237_2
  • xorg-libice=1.0.9=h470a237_4
  • xorg-libsm=1.2.3=h8c8a85c_0
  • xorg-libx11=1.6.6=h470a237_0
  • xorg-libxau=1.0.8=h470a237_6
  • xorg-libxdmcp=1.1.2=h470a237_7
  • xorg-libxext=1.3.3=h470a237_4
  • xorg-libxrender=0.9.10=h470a237_2
  • xorg-libxt=1.1.5=h470a237_2
  • xorg-renderproto=0.11.1=h470a237_2
  • xorg-xextproto=7.3.0=h470a237_2
  • xorg-xproto=7.0.31=h470a237_7
  • xz=5.2.4=h470a237_1
  • zlib=1.2.11=h470a237_3
  • libgcc-ng=7.3.0=hdf63c60_0
  • _r-mutex=1.0.0=anacondar_1
  • blas=1.0=mkl
  • gsl=2.2.1=h0c605f7_3
  • intel-openmp=2019.1=144
  • mkl=2019.1=144
  • wget=1.19.5=h1ad7b7a_0
multiqc 1
  • results/qc/hg38/multiqc.html
  • multiqc ==1.2
  • networkx <2.0
edegR_deg 30
  • results/deg/edegR/hg38/PE/unique/count_NSQ-vs-HSQ_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/unique/count_NSQ-vs-HSQ_edegR_Res.csv
  • results/deg/edegR/hg38/PE/unique/count_NSQ-vs-HSQ_edegR_Res.rds
  • results/deg/edegR/hg38/PE/fraction/count_NSQ-vs-HSQ_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/fraction/count_NSQ-vs-HSQ_edegR_Res.csv
  • results/deg/edegR/hg38/PE/fraction/count_NSQ-vs-HSQ_edegR_Res.rds
  • results/deg/edegR/hg38/PE/all/count_NSQ-vs-HSQ_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/all/count_NSQ-vs-HSQ_edegR_Res.csv
  • results/deg/edegR/hg38/PE/all/count_NSQ-vs-HSQ_edegR_Res.rds
  • results/deg/edegR/hg38/PE/salmonAlignment/estcount_NSQ-vs-HSQ_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/salmonAlignment/estcount_NSQ-vs-HSQ_edegR_Res.csv
  • results/deg/edegR/hg38/PE/salmonAlignment/estcount_NSQ-vs-HSQ_edegR_Res.rds
  • results/deg/edegR/hg38/PE/salmonReads/estcount_NSQ-vs-HSQ_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/salmonReads/estcount_NSQ-vs-HSQ_edegR_Res.csv
  • results/deg/edegR/hg38/PE/salmonReads/estcount_NSQ-vs-HSQ_edegR_Res.rds
  • results/deg/edegR/hg38/PE/unique/count_NSQ-vs-NSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/unique/count_NSQ-vs-NSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/unique/count_NSQ-vs-NSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/fraction/count_NSQ-vs-NSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/fraction/count_NSQ-vs-NSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/fraction/count_NSQ-vs-NSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/all/count_NSQ-vs-NSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/all/count_NSQ-vs-NSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/all/count_NSQ-vs-NSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/salmonAlignment/estcount_NSQ-vs-NSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/salmonAlignment/estcount_NSQ-vs-NSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/salmonAlignment/estcount_NSQ-vs-NSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/salmonReads/estcount_NSQ-vs-NSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/salmonReads/estcount_NSQ-vs-NSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/salmonReads/estcount_NSQ-vs-NSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/unique/count_NSQ-vs-HSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/unique/count_NSQ-vs-HSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/unique/count_NSQ-vs-HSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/fraction/count_NSQ-vs-HSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/fraction/count_NSQ-vs-HSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/fraction/count_NSQ-vs-HSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/all/count_NSQ-vs-HSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/all/count_NSQ-vs-HSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/all/count_NSQ-vs-HSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/salmonAlignment/estcount_NSQ-vs-HSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/salmonAlignment/estcount_NSQ-vs-HSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/salmonAlignment/estcount_NSQ-vs-HSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/salmonReads/estcount_NSQ-vs-HSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/salmonReads/estcount_NSQ-vs-HSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/salmonReads/estcount_NSQ-vs-HSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/unique/count_HSQ-vs-NSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/unique/count_HSQ-vs-NSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/unique/count_HSQ-vs-NSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/fraction/count_HSQ-vs-NSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/fraction/count_HSQ-vs-NSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/fraction/count_HSQ-vs-NSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/all/count_HSQ-vs-NSQsi_edegR_ResData.rds
  • results/deg/edegR/hg38/PE/all/count_HSQ-vs-NSQsi_edegR_Res.csv
  • results/deg/edegR/hg38/PE/all/count_HSQ-vs-NSQsi_edegR_Res.rds
  • results/deg/edegR/hg38/PE/salmonAlignment/estcount_HSQ-vs-NSQsi_edegR_ResData.rds
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edegR_plot_global 5
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  • results/plot/edegR/hg38_PE_salmonAlignment_estcount_edegR_plot_MDS.png
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build_R_package 1
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  • r-reshape2=1.4.3=r351h9d2a408_2
  • r-rlang=0.3.0.1=r351h470a237_0
  • r-rmarkdown=1.10=r351h6115d3f_1001
  • r-rpart=4.1_13=r351hc070d10_2
  • r-rprojroot=1.3_2=r351h6115d3f_1001
  • r-rsqlite=2.1.1=r351h9d2a408_0
  • r-rstudioapi=0.7=r351h6115d3f_1001
  • r-rvest=0.3.2=r351h6115d3f_1001
  • r-scales=1.0.0=r351h9d2a408_1
  • r-selectr=0.4_1=r351h6115d3f_1000
  • r-snow=0.4_3=r351h6115d3f_1000
  • r-stringi=1.2.4=r351h9d2a408_1
  • r-stringr=1.3.1=r351h6115d3f_1001
  • r-survival=2.42_6=r351hc070d10_1
  • r-tibble=1.4.2=r351hc070d10_2
  • r-tidyr=0.8.1=r351h9d2a408_2
  • r-tidyselect=0.2.4=r351h9d2a408_3
  • r-tidyverse=1.2.1=r351h6115d3f_1001
  • r-tinytex=0.8=r351h6115d3f_1000
  • r-utf8=1.1.4=r351hc070d10_0
  • r-vcd=1.4_4=r351h6115d3f_1001
  • r-viridis=0.5.1=r351h6115d3f_1001
  • r-viridislite=0.3.0=r351h6115d3f_1001
  • r-whisker=0.3_2=r351h6115d3f_1001
  • r-withr=2.1.2=r351h6115d3f_1000
  • r-xfun=0.3=r351h6115d3f_1001
  • r-xml=3.98_1.16=r351hc070d10_0
  • r-xml2=1.2.0=r351h9d2a408_2
  • r-xtable=1.8_3=r351_2000
  • r-yaml=2.2.0=r351hc070d10_1
  • r-zoo=1.8_3=r351hc070d10_0
  • readline=7.0=haf1bffa_1
  • tk=8.6.9=ha92aebf_0
  • xorg-kbproto=1.0.7=h470a237_2
  • xorg-libice=1.0.9=h470a237_4
  • xorg-libsm=1.2.3=h8c8a85c_0
  • xorg-libx11=1.6.6=h470a237_0
  • xorg-libxau=1.0.8=h470a237_6
  • xorg-libxdmcp=1.1.2=h470a237_7
  • xorg-libxext=1.3.3=h470a237_4
  • xorg-libxrender=0.9.10=h470a237_2
  • xorg-libxt=1.1.5=h470a237_2
  • xorg-renderproto=0.11.1=h470a237_2
  • xorg-xextproto=7.3.0=h470a237_2
  • xorg-xproto=7.0.31=h470a237_7
  • xz=5.2.4=h470a237_1
  • zlib=1.2.11=h470a237_3
  • libgcc-ng=7.3.0=hdf63c60_0
  • _r-mutex=1.0.0=anacondar_1
  • blas=1.0=mkl
  • gsl=2.2.1=h0c605f7_3
  • intel-openmp=2019.1=144
  • mkl=2019.1=144
  • wget=1.19.5=h1ad7b7a_0
cutadapt_pe 16
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  • results/trimmed/cutadapt/MK_1-NSQ_1.2.fastq.gz
  • results/trimmed/cutadapt/MK_1-NSQ_1.qc.txt
  • results/trimmed/cutadapt/MK_2-NSQsi_1.1.fastq.gz
  • results/trimmed/cutadapt/MK_2-NSQsi_1.2.fastq.gz
  • results/trimmed/cutadapt/MK_2-NSQsi_1.qc.txt
  • results/trimmed/cutadapt/MK_3-HSQ_1.1.fastq.gz
  • results/trimmed/cutadapt/MK_3-HSQ_1.2.fastq.gz
  • results/trimmed/cutadapt/MK_3-HSQ_1.qc.txt
  • results/trimmed/cutadapt/MK_4-HSQsi_1.1.fastq.gz
  • results/trimmed/cutadapt/MK_4-HSQsi_1.2.fastq.gz
  • results/trimmed/cutadapt/MK_4-HSQsi_1.qc.txt
  • results/trimmed/cutadapt/MK_5-NSQ_2.1.fastq.gz
  • results/trimmed/cutadapt/MK_5-NSQ_2.2.fastq.gz
  • results/trimmed/cutadapt/MK_5-NSQ_2.qc.txt
  • results/trimmed/cutadapt/MK_6-NSQsi_2.1.fastq.gz
  • results/trimmed/cutadapt/MK_6-NSQsi_2.2.fastq.gz
  • results/trimmed/cutadapt/MK_6-NSQsi_2.qc.txt
  • results/trimmed/cutadapt/MK_7-HSQ_2.1.fastq.gz
  • results/trimmed/cutadapt/MK_7-HSQ_2.2.fastq.gz
  • results/trimmed/cutadapt/MK_7-HSQ_2.qc.txt
  • results/trimmed/cutadapt/MK_8-HSQsi_2.1.fastq.gz
  • results/trimmed/cutadapt/MK_8-HSQsi_2.2.fastq.gz
  • results/trimmed/cutadapt/MK_8-HSQsi_2.qc.txt
  • results/trimmed/cutadapt/MK_9-NSQ_3.1.fastq.gz
  • results/trimmed/cutadapt/MK_9-NSQ_3.2.fastq.gz
  • results/trimmed/cutadapt/MK_9-NSQ_3.qc.txt
  • results/trimmed/cutadapt/MK_10-NSQsi_3.1.fastq.gz
  • results/trimmed/cutadapt/MK_10-NSQsi_3.2.fastq.gz
  • results/trimmed/cutadapt/MK_10-NSQsi_3.qc.txt
  • results/trimmed/cutadapt/MK_11-HSQ_3.1.fastq.gz
  • results/trimmed/cutadapt/MK_11-HSQ_3.2.fastq.gz
  • results/trimmed/cutadapt/MK_11-HSQ_3.qc.txt
  • results/trimmed/cutadapt/MK_12-HSQsi_3.1.fastq.gz
  • results/trimmed/cutadapt/MK_12-HSQsi_3.2.fastq.gz
  • results/trimmed/cutadapt/MK_12-HSQsi_3.qc.txt
  • results/trimmed/cutadapt/MK_13-NSQ_4.1.fastq.gz
  • results/trimmed/cutadapt/MK_13-NSQ_4.2.fastq.gz
  • results/trimmed/cutadapt/MK_13-NSQ_4.qc.txt
  • results/trimmed/cutadapt/MK_14-NSQsi_4.1.fastq.gz
  • results/trimmed/cutadapt/MK_14-NSQsi_4.2.fastq.gz
  • results/trimmed/cutadapt/MK_14-NSQsi_4.qc.txt
  • results/trimmed/cutadapt/MK_15-HSQ_4.1.fastq.gz
  • results/trimmed/cutadapt/MK_15-HSQ_4.2.fastq.gz
  • results/trimmed/cutadapt/MK_15-HSQ_4.qc.txt
  • results/trimmed/cutadapt/MK_16-HSQsi_4.1.fastq.gz
  • results/trimmed/cutadapt/MK_16-HSQsi_4.2.fastq.gz
  • results/trimmed/cutadapt/MK_16-HSQsi_4.qc.txt
  • cutadapt ==1.18
samtools_stats 16
  • results/qc/samtools-stats/hg38/MK_1-NSQ_1.txt
  • results/qc/samtools-stats/hg38/MK_2-NSQsi_1.txt
  • results/qc/samtools-stats/hg38/MK_3-HSQ_1.txt
  • results/qc/samtools-stats/hg38/MK_4-HSQsi_1.txt
  • results/qc/samtools-stats/hg38/MK_5-NSQ_2.txt
  • results/qc/samtools-stats/hg38/MK_6-NSQsi_2.txt
  • results/qc/samtools-stats/hg38/MK_7-HSQ_2.txt
  • results/qc/samtools-stats/hg38/MK_8-HSQsi_2.txt
  • results/qc/samtools-stats/hg38/MK_9-NSQ_3.txt
  • results/qc/samtools-stats/hg38/MK_10-NSQsi_3.txt
  • results/qc/samtools-stats/hg38/MK_11-HSQ_3.txt
  • results/qc/samtools-stats/hg38/MK_12-HSQsi_3.txt
  • results/qc/samtools-stats/hg38/MK_13-NSQ_4.txt
  • results/qc/samtools-stats/hg38/MK_14-NSQsi_4.txt
  • results/qc/samtools-stats/hg38/MK_15-HSQ_4.txt
  • results/qc/samtools-stats/hg38/MK_16-HSQsi_4.txt
  • samtools ==1.6
fastqc_q1 16
  • results/qc/fastqc/MK_1-NSQ_1_R1.html
  • results/qc/fastqc/MK_1-NSQ_1_R1_fastqc.zip
  • results/qc/fastqc/MK_2-NSQsi_1_R1.html
  • results/qc/fastqc/MK_2-NSQsi_1_R1_fastqc.zip
  • results/qc/fastqc/MK_3-HSQ_1_R1.html
  • results/qc/fastqc/MK_3-HSQ_1_R1_fastqc.zip
  • results/qc/fastqc/MK_4-HSQsi_1_R1.html
  • results/qc/fastqc/MK_4-HSQsi_1_R1_fastqc.zip
  • results/qc/fastqc/MK_5-NSQ_2_R1.html
  • results/qc/fastqc/MK_5-NSQ_2_R1_fastqc.zip
  • results/qc/fastqc/MK_6-NSQsi_2_R1.html
  • results/qc/fastqc/MK_6-NSQsi_2_R1_fastqc.zip
  • results/qc/fastqc/MK_7-HSQ_2_R1.html
  • results/qc/fastqc/MK_7-HSQ_2_R1_fastqc.zip
  • results/qc/fastqc/MK_8-HSQsi_2_R1.html
  • results/qc/fastqc/MK_8-HSQsi_2_R1_fastqc.zip
  • results/qc/fastqc/MK_9-NSQ_3_R1.html
  • results/qc/fastqc/MK_9-NSQ_3_R1_fastqc.zip
  • results/qc/fastqc/MK_10-NSQsi_3_R1.html
  • results/qc/fastqc/MK_10-NSQsi_3_R1_fastqc.zip
  • results/qc/fastqc/MK_11-HSQ_3_R1.html
  • results/qc/fastqc/MK_11-HSQ_3_R1_fastqc.zip
  • results/qc/fastqc/MK_12-HSQsi_3_R1.html
  • results/qc/fastqc/MK_12-HSQsi_3_R1_fastqc.zip
  • results/qc/fastqc/MK_13-NSQ_4_R1.html
  • results/qc/fastqc/MK_13-NSQ_4_R1_fastqc.zip
  • results/qc/fastqc/MK_14-NSQsi_4_R1.html
  • results/qc/fastqc/MK_14-NSQsi_4_R1_fastqc.zip
  • results/qc/fastqc/MK_15-HSQ_4_R1.html
  • results/qc/fastqc/MK_15-HSQ_4_R1_fastqc.zip
  • results/qc/fastqc/MK_16-HSQsi_4_R1.html
  • results/qc/fastqc/MK_16-HSQsi_4_R1_fastqc.zip
  • fastqc ==0.11.5
  • fontconfig ==2.12.1
fastqc_q2 16
  • results/qc/fastqc/MK_1-NSQ_1_R2.html
  • results/qc/fastqc/MK_1-NSQ_1_R2_fastqc.zip
  • results/qc/fastqc/MK_2-NSQsi_1_R2.html
  • results/qc/fastqc/MK_2-NSQsi_1_R2_fastqc.zip
  • results/qc/fastqc/MK_3-HSQ_1_R2.html
  • results/qc/fastqc/MK_3-HSQ_1_R2_fastqc.zip
  • results/qc/fastqc/MK_4-HSQsi_1_R2.html
  • results/qc/fastqc/MK_4-HSQsi_1_R2_fastqc.zip
  • results/qc/fastqc/MK_5-NSQ_2_R2.html
  • results/qc/fastqc/MK_5-NSQ_2_R2_fastqc.zip
  • results/qc/fastqc/MK_6-NSQsi_2_R2.html
  • results/qc/fastqc/MK_6-NSQsi_2_R2_fastqc.zip
  • results/qc/fastqc/MK_7-HSQ_2_R2.html
  • results/qc/fastqc/MK_7-HSQ_2_R2_fastqc.zip
  • results/qc/fastqc/MK_8-HSQsi_2_R2.html
  • results/qc/fastqc/MK_8-HSQsi_2_R2_fastqc.zip
  • results/qc/fastqc/MK_9-NSQ_3_R2.html
  • results/qc/fastqc/MK_9-NSQ_3_R2_fastqc.zip
  • results/qc/fastqc/MK_10-NSQsi_3_R2.html
  • results/qc/fastqc/MK_10-NSQsi_3_R2_fastqc.zip
  • results/qc/fastqc/MK_11-HSQ_3_R2.html
  • results/qc/fastqc/MK_11-HSQ_3_R2_fastqc.zip
  • results/qc/fastqc/MK_12-HSQsi_3_R2.html
  • results/qc/fastqc/MK_12-HSQsi_3_R2_fastqc.zip
  • results/qc/fastqc/MK_13-NSQ_4_R2.html
  • results/qc/fastqc/MK_13-NSQ_4_R2_fastqc.zip
  • results/qc/fastqc/MK_14-NSQsi_4_R2.html
  • results/qc/fastqc/MK_14-NSQsi_4_R2_fastqc.zip
  • results/qc/fastqc/MK_15-HSQ_4_R2.html
  • results/qc/fastqc/MK_15-HSQ_4_R2_fastqc.zip
  • results/qc/fastqc/MK_16-HSQsi_4_R2.html
  • results/qc/fastqc/MK_16-HSQsi_4_R2_fastqc.zip
  • fastqc ==0.11.5
  • fontconfig ==2.12.1
featureCounts 48
  • results/quantification/featureCounts/hg38/PE/unique/MK_1-NSQ_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_1-NSQ_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_2-NSQsi_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_2-NSQsi_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_3-HSQ_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_3-HSQ_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_4-HSQsi_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_4-HSQsi_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_5-NSQ_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_5-NSQ_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_6-NSQsi_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_6-NSQsi_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_7-HSQ_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_7-HSQ_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_8-HSQsi_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_8-HSQsi_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_9-NSQ_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_9-NSQ_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_10-NSQsi_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_10-NSQsi_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_11-HSQ_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_11-HSQ_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_12-HSQsi_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_12-HSQsi_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_13-NSQ_4/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_13-NSQ_4/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_14-NSQsi_4/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_14-NSQsi_4/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_15-HSQ_4/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_15-HSQ_4/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/unique/MK_16-HSQsi_4/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/unique/MK_16-HSQsi_4/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_1-NSQ_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_1-NSQ_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_2-NSQsi_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_2-NSQsi_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_3-HSQ_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_3-HSQ_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_4-HSQsi_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_4-HSQsi_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_5-NSQ_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_5-NSQ_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_6-NSQsi_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_6-NSQsi_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_7-HSQ_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_7-HSQ_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_8-HSQsi_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_8-HSQsi_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_9-NSQ_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_9-NSQ_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_10-NSQsi_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_10-NSQsi_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_11-HSQ_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_11-HSQ_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_12-HSQsi_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_12-HSQsi_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_13-NSQ_4/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_13-NSQ_4/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_14-NSQsi_4/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_14-NSQsi_4/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_15-HSQ_4/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_15-HSQ_4/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/fraction/MK_16-HSQsi_4/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/fraction/MK_16-HSQsi_4/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_1-NSQ_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_1-NSQ_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_2-NSQsi_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_2-NSQsi_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_3-HSQ_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_3-HSQ_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_4-HSQsi_1/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_4-HSQsi_1/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_5-NSQ_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_5-NSQ_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_6-NSQsi_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_6-NSQsi_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_7-HSQ_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_7-HSQ_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_8-HSQsi_2/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_8-HSQsi_2/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_9-NSQ_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_9-NSQ_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_10-NSQsi_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_10-NSQsi_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_11-HSQ_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_11-HSQ_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_12-HSQsi_3/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_12-HSQsi_3/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_13-NSQ_4/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_13-NSQ_4/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_14-NSQsi_4/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_14-NSQsi_4/feature_counts.result.summary
  • results/quantification/featureCounts/hg38/PE/all/MK_15-HSQ_4/feature_counts.result
  • results/quantification/featureCounts/hg38/PE/all/MK_15-HSQ_4/feature_counts.result.summary
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  • results/quantification/featureCounts/hg38/PE/all/MK_16-HSQsi_4/feature_counts.result.summary
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  • r-gtable=0.2.0=r351h6115d3f_1001
  • r-gtools=3.8.1=r351hc070d10_2
  • r-haven=1.1.2=r351h9d2a408_2
  • r-highr=0.7=r351h6115d3f_1001
  • r-hmisc=4.1_1=r351h364d78e_1
  • r-hms=0.4.2=r351h6115d3f_1000
  • r-htmltable=1.12=r351h6115d3f_1000
  • r-htmltools=0.3.6=r351hfc679d8_2
  • r-htmlwidgets=1.2=r351h6115d3f_1000
  • r-httr=1.3.1=r351h6115d3f_1001
  • r-hwriter=1.3.2=r351h6115d3f_1001
  • r-intervals=0.15.1=r351h9d2a408_2
  • r-jsonlite=1.5=r351hc070d10_2
  • r-kernsmooth=2.23_15=r351h364d78e_2
  • r-knitr=1.20=r351h6115d3f_1001
  • r-labeling=0.3=r351h6115d3f_1001
  • r-lambda.r=1.2.3=r351h6115d3f_1000
  • r-lattice=0.20_35=r351hc070d10_0
  • r-latticeextra=0.6_28=r351h6115d3f_1001
  • r-lazyeval=0.2.1=r351hc070d10_2
  • r-listenv=0.7.0=r351h6115d3f_1001
  • r-lmtest=0.9_36=r351h364d78e_0
  • r-locfit=1.5_9.1=r351h470a237_2
  • r-lsd=3.0=r351_1001
  • r-lsei=1.2_0=r351ha44fe06_2
  • r-lubridate=1.7.4=r351h9d2a408_1
  • r-magrittr=1.5=r351h6115d3f_1001
  • r-markdown=0.8=r351hc070d10_3
  • r-mass=7.3_50=r351hc070d10_2
  • r-matrix=1.2_14=r351hc070d10_2
  • r-matrixstats=0.54.0=r351hc070d10_0
  • r-memoise=1.1.0=r351h6115d3f_1001
  • r-mgcv=1.8_24=r351hc070d10_2
  • r-mime=0.5=r351hc070d10_2
  • r-modelr=0.1.2=r351h6115d3f_1001
  • r-munsell=0.5.0=r351h6115d3f_1001
  • r-nlme=3.1_137=r351h364d78e_0
  • r-nnet=7.3_12=r351hc070d10_2
  • r-npsurv=0.4_0=r351h6115d3f_1000
  • r-openssl=1.0.2=r351h9f97512_0
  • r-pillar=1.3.0=r351h6115d3f_1000
  • r-pkgconfig=2.0.2=r351h6115d3f_1001
  • r-plogr=0.2.0=r351h6115d3f_1001
  • r-plyr=1.8.4=r351h9d2a408_2
  • r-prettyunits=1.0.2=r351h6115d3f_1001
  • r-processx=3.2.0=r351hc070d10_1
  • r-progress=1.2.0=r351h6115d3f_1002
  • r-ps=1.1.0=r351hc070d10_1
  • r-purrr=0.2.5=r351hc070d10_2
  • r-r6=2.2.2=r351h6115d3f_1001
  • r-rcolorbrewer=1.1_2=r351h6115d3f_1001
  • r-rcpp=1.0.0=r351h9d2a408_0
  • r-rcpparmadillo=0.9.100.5.0=r351h9d2a408_0
  • r-rcurl=1.95_4.11=r351h86b9717_2
  • r-readr=1.1.1=r351h9d2a408_2
  • r-readxl=1.1.0=r351h9d2a408_2
  • r-rematch=1.0.1=r351h6115d3f_1001
  • r-reprex=0.2.0=r351h6115d3f_1001
  • r-reshape2=1.4.3=r351h9d2a408_2
  • r-rlang=0.3.0.1=r351h470a237_0
  • r-rmarkdown=1.10=r351h6115d3f_1001
  • r-rpart=4.1_13=r351hc070d10_2
  • r-rprojroot=1.3_2=r351h6115d3f_1001
  • r-rsqlite=2.1.1=r351h9d2a408_0
  • r-rstudioapi=0.7=r351h6115d3f_1001
  • r-rvest=0.3.2=r351h6115d3f_1001
  • r-scales=1.0.0=r351h9d2a408_1
  • r-selectr=0.4_1=r351h6115d3f_1000
  • r-snow=0.4_3=r351h6115d3f_1000
  • r-stringi=1.2.4=r351h9d2a408_1
  • r-stringr=1.3.1=r351h6115d3f_1001
  • r-survival=2.42_6=r351hc070d10_1
  • r-tibble=1.4.2=r351hc070d10_2
  • r-tidyr=0.8.1=r351h9d2a408_2
  • r-tidyselect=0.2.4=r351h9d2a408_3
  • r-tidyverse=1.2.1=r351h6115d3f_1001
  • r-tinytex=0.8=r351h6115d3f_1000
  • r-utf8=1.1.4=r351hc070d10_0
  • r-vcd=1.4_4=r351h6115d3f_1001
  • r-viridis=0.5.1=r351h6115d3f_1001
  • r-viridislite=0.3.0=r351h6115d3f_1001
  • r-whisker=0.3_2=r351h6115d3f_1001
  • r-withr=2.1.2=r351h6115d3f_1000
  • r-xfun=0.3=r351h6115d3f_1001
  • r-xml=3.98_1.16=r351hc070d10_0
  • r-xml2=1.2.0=r351h9d2a408_2
  • r-xtable=1.8_3=r351_2000
  • r-yaml=2.2.0=r351hc070d10_1
  • r-zoo=1.8_3=r351hc070d10_0
  • readline=7.0=haf1bffa_1
  • tk=8.6.9=ha92aebf_0
  • xorg-kbproto=1.0.7=h470a237_2
  • xorg-libice=1.0.9=h470a237_4
  • xorg-libsm=1.2.3=h8c8a85c_0
  • xorg-libx11=1.6.6=h470a237_0
  • xorg-libxau=1.0.8=h470a237_6
  • xorg-libxdmcp=1.1.2=h470a237_7
  • xorg-libxext=1.3.3=h470a237_4
  • xorg-libxrender=0.9.10=h470a237_2
  • xorg-libxt=1.1.5=h470a237_2
  • xorg-renderproto=0.11.1=h470a237_2
  • xorg-xextproto=7.3.0=h470a237_2
  • xorg-xproto=7.0.31=h470a237_7
  • xz=5.2.4=h470a237_1
  • zlib=1.2.11=h470a237_3
  • libgcc-ng=7.3.0=hdf63c60_0
  • _r-mutex=1.0.0=anacondar_1
  • blas=1.0=mkl
  • gsl=2.2.1=h0c605f7_3
  • intel-openmp=2019.1=144
  • mkl=2019.1=144
  • wget=1.19.5=h1ad7b7a_0
sambamba_sort 16
  • results/mapping/star/hg38/MK_1-NSQ_1/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_2-NSQsi_1/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_3-HSQ_1/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_4-HSQsi_1/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_5-NSQ_2/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_6-NSQsi_2/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_7-HSQ_2/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_8-HSQsi_2/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_9-NSQ_3/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_10-NSQsi_3/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_11-HSQ_3/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_12-HSQsi_3/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_13-NSQ_4/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_14-NSQsi_4/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_15-HSQ_4/Aligned.out.sorted.bam
  • results/mapping/star/hg38/MK_16-HSQsi_4/Aligned.out.sorted.bam
  • sambamba ==0.6.6
TximporTrGe 1
  • results/quantification/counts/hg38/TrGe.csv
  • results/quantification/counts/hg38/TrGe.rds
  • r-venndiagram=1.6.20
  • bioconductor-annotate=1.58.0=r351_0
  • bioconductor-annotationdbi=1.42.1=r351_0
  • bioconductor-biobase=2.40.0=r351h470a237_0
  • bioconductor-biocgenerics=0.26.0=r351_0
  • bioconductor-biocparallel=1.14.2=r351h26a2512_0
  • bioconductor-biomart=2.36.1=r351_0
  • bioconductor-biostrings=2.48.0=r351h470a237_0
  • bioconductor-bsgenome=1.48.0=r351_0
  • bioconductor-delayedarray=0.6.6=r351_0
  • bioconductor-deseq=1.32.0=r351h470a237_0
  • bioconductor-deseq2=1.20.0=r351hfc679d8_0
  • bioconductor-easyrnaseq=2.16.0=r351_0
  • bioconductor-edger=3.22.5=r351hfc679d8_0
  • bioconductor-genefilter=1.62.0=r351h26a2512_0
  • bioconductor-geneplotter=1.58.0=r351_0
  • bioconductor-genomeinfodb=1.16.0=r351_0
  • bioconductor-genomeinfodbdata=1.1.0=r351_0
  • bioconductor-genomeintervals=1.36.0=r351_0
  • bioconductor-genomicalignments=1.16.0=r351h470a237_0
  • bioconductor-genomicfeatures=1.32.3=r351_0
  • bioconductor-genomicranges=1.32.7=r351h470a237_0
  • bioconductor-iranges=2.14.12=r351h470a237_0
  • bioconductor-limma=3.36.5=r351h470a237_0
  • bioconductor-rsamtools=1.32.3=r351hfc679d8_0
  • bioconductor-rtracklayer=1.40.6=r351h470a237_0
  • bioconductor-s4vectors=0.18.3=r351h470a237_0
  • bioconductor-shortread=1.38.0=r351hfc679d8_0
  • bioconductor-summarizedexperiment=1.10.1=r351_0
  • bioconductor-tximport=1.8.0=r351_0
  • bioconductor-xvector=0.20.0=r351h470a237_0
  • bioconductor-zlibbioc=1.26.0=r351h470a237_0
  • r-data.table=1.11.6=r351hc070d10_0
  • bzip2=1.0.6=h470a237_2
  • ca-certificates=2018.11.29=ha4d7672_0
  • cairo=1.14.12=h276e583_5
  • curl=7.61.0=h93b3f91_2
  • fontconfig=2.13.1=h65d0f4c_0
  • freetype=2.9.1=h6debe1e_4
  • gettext=0.19.8.1=h5e8e0c9_1
  • glib=2.56.2=h464dc38_1
  • gmp=6.1.2=hfc679d8_0
  • graphite2=1.3.12=hfc679d8_1
  • harfbuzz=1.9.0=h04dbb29_1
  • icu=58.2=hfc679d8_0
  • jpeg=9c=h470a237_1
  • krb5=1.14.6=0
  • lapack=3.6.1=1
  • libffi=3.2.1=hfc679d8_5
  • libgfortran=3.0.0=1
  • libiconv=1.15=h470a237_3
  • libpng=1.6.36=ha92aebf_0
  • libssh2=1.8.0=h5b517e9_3
  • libstdcxx-ng=7.2.0=hdf63c60_3
  • libtiff=4.0.10=he6b73bb_0
  • libuuid=2.32.1=h470a237_2
  • libxcb=1.13=h470a237_2
  • libxml2=2.9.8=h422b904_5
  • ncurses=6.1=hfc679d8_1
  • openblas=0.2.20=8
  • openssl=1.0.2p=h470a237_1
  • pandoc=2.5=0
  • pango=1.40.14=he752989_2
  • pcre=8.41=hfc679d8_3
  • pixman=0.34.0=h470a237_3
  • pthread-stubs=0.4=h470a237_1
  • r-acepack=1.4.1=r351h364d78e_2
  • r-assertthat=0.2.0=r351h6115d3f_1001
  • r-backports=1.1.2=r351hc070d10_1
  • r-base=3.5.1=h4fe35fd_1
  • r-base64enc=0.1_3=r351hc070d10_2
  • r-bh=1.66.0_1=r351_2001
  • r-bindr=0.1.1=r351h6115d3f_1001
  • r-bindrcpp=0.2.2=r351h9d2a408_1
  • r-bit=1.1_12=r351h470a237_2
  • r-bit64=0.9_7=r351hc070d10_0
  • r-bitops=1.0_6=r351hc070d10_2
  • r-blob=1.1.1=r351_1001
  • r-broom=0.5.0=r351h6115d3f_1002
  • r-callr=3.0.0=r351h6115d3f_1000
  • r-catools=1.17.1.1=r351h9d2a408_2
  • r-cellranger=1.1.0=r351h6115d3f_1001
  • r-checkmate=1.8.5=r351hc070d10_2
  • r-cli=1.0.0=r351h6115d3f_1001
  • r-clipr=0.4.1=r351h6115d3f_1001
  • r-cluster=2.0.7_1=r351h364d78e_0
  • r-codetools=0.2_15=r351h6115d3f_1001
  • r-colorspace=1.3_2=r351hc070d10_2
  • r-cowplot=0.9.3=r351h6115d3f_1001
  • r-crayon=1.3.4=r351h6115d3f_1001
  • r-curl=3.2=r351hc070d10_2
  • r-dbi=1.0.0=r351h6115d3f_1001
  • r-dbplyr=1.2.2=r351h6115d3f_1001
  • r-digest=0.6.18=r351hc070d10_0
  • r-dplyr=0.7.6=r351h9d2a408_1
  • r-evaluate=0.11=r351h6115d3f_1000
  • r-fansi=0.3.0=r351hc070d10_0
  • r-fitdistrplus=1.0_11=r351h6115d3f_1000
  • r-forcats=0.3.0=r351h6115d3f_1001
  • r-foreign=0.8_71=r351hc070d10_2
  • r-formatr=1.5=r351h6115d3f_1001
  • r-formula=1.2_3=r351h6115d3f_1001
  • r-furrr=0.1.0=r351h6115d3f_1000
  • r-futile.logger=1.4.3=r351h6115d3f_1001
  • r-futile.options=1.0.1=r351h6115d3f_1000
  • r-future=1.10.0=r351h6115d3f_1000
  • r-gdata=2.18.0=r351h6115d3f_1001
  • r-ggplot2=3.1.0=r351h6115d3f_1000
  • r-globals=0.12.2=r351h6115d3f_1000
  • r-glue=1.3.0=r351h470a237_2
  • r-gplots=3.0.1=r351h6115d3f_1001
  • r-gridextra=2.3=r351h6115d3f_1001
  • r-gtable=0.2.0=r351h6115d3f_1001
  • r-gtools=3.8.1=r351hc070d10_2
  • r-haven=1.1.2=r351h9d2a408_2
  • r-highr=0.7=r351h6115d3f_1001
  • r-hmisc=4.1_1=r351h364d78e_1
  • r-hms=0.4.2=r351h6115d3f_1000
  • r-htmltable=1.12=r351h6115d3f_1000
  • r-htmltools=0.3.6=r351hfc679d8_2
  • r-htmlwidgets=1.2=r351h6115d3f_1000
  • r-httr=1.3.1=r351h6115d3f_1001
  • r-hwriter=1.3.2=r351h6115d3f_1001
  • r-intervals=0.15.1=r351h9d2a408_2
  • r-jsonlite=1.5=r351hc070d10_2
  • r-kernsmooth=2.23_15=r351h364d78e_2
  • r-knitr=1.20=r351h6115d3f_1001
  • r-labeling=0.3=r351h6115d3f_1001
  • r-lambda.r=1.2.3=r351h6115d3f_1000
  • r-lattice=0.20_35=r351hc070d10_0
  • r-latticeextra=0.6_28=r351h6115d3f_1001
  • r-lazyeval=0.2.1=r351hc070d10_2
  • r-listenv=0.7.0=r351h6115d3f_1001
  • r-lmtest=0.9_36=r351h364d78e_0
  • r-locfit=1.5_9.1=r351h470a237_2
  • r-lsd=3.0=r351_1001
  • r-lsei=1.2_0=r351ha44fe06_2
  • r-lubridate=1.7.4=r351h9d2a408_1
  • r-magrittr=1.5=r351h6115d3f_1001
  • r-markdown=0.8=r351hc070d10_3
  • r-mass=7.3_50=r351hc070d10_2
  • r-matrix=1.2_14=r351hc070d10_2
  • r-matrixstats=0.54.0=r351hc070d10_0
  • r-memoise=1.1.0=r351h6115d3f_1001
  • r-mgcv=1.8_24=r351hc070d10_2
  • r-mime=0.5=r351hc070d10_2
  • r-modelr=0.1.2=r351h6115d3f_1001
  • r-munsell=0.5.0=r351h6115d3f_1001
  • r-nlme=3.1_137=r351h364d78e_0
  • r-nnet=7.3_12=r351hc070d10_2
  • r-npsurv=0.4_0=r351h6115d3f_1000
  • r-openssl=1.0.2=r351h9f97512_0
  • r-pillar=1.3.0=r351h6115d3f_1000
  • r-pkgconfig=2.0.2=r351h6115d3f_1001
  • r-plogr=0.2.0=r351h6115d3f_1001
  • r-plyr=1.8.4=r351h9d2a408_2
  • r-prettyunits=1.0.2=r351h6115d3f_1001
  • r-processx=3.2.0=r351hc070d10_1
  • r-progress=1.2.0=r351h6115d3f_1002
  • r-ps=1.1.0=r351hc070d10_1
  • r-purrr=0.2.5=r351hc070d10_2
  • r-r6=2.2.2=r351h6115d3f_1001
  • r-rcolorbrewer=1.1_2=r351h6115d3f_1001
  • r-rcpp=1.0.0=r351h9d2a408_0
  • r-rcpparmadillo=0.9.100.5.0=r351h9d2a408_0
  • r-rcurl=1.95_4.11=r351h86b9717_2
  • r-readr=1.1.1=r351h9d2a408_2
  • r-readxl=1.1.0=r351h9d2a408_2
  • r-rematch=1.0.1=r351h6115d3f_1001
  • r-reprex=0.2.0=r351h6115d3f_1001
  • r-reshape2=1.4.3=r351h9d2a408_2
  • r-rlang=0.3.0.1=r351h470a237_0
  • r-rmarkdown=1.10=r351h6115d3f_1001
  • r-rpart=4.1_13=r351hc070d10_2
  • r-rprojroot=1.3_2=r351h6115d3f_1001
  • r-rsqlite=2.1.1=r351h9d2a408_0
  • r-rstudioapi=0.7=r351h6115d3f_1001
  • r-rvest=0.3.2=r351h6115d3f_1001
  • r-scales=1.0.0=r351h9d2a408_1
  • r-selectr=0.4_1=r351h6115d3f_1000
  • r-snow=0.4_3=r351h6115d3f_1000
  • r-stringi=1.2.4=r351h9d2a408_1
  • r-stringr=1.3.1=r351h6115d3f_1001
  • r-survival=2.42_6=r351hc070d10_1
  • r-tibble=1.4.2=r351hc070d10_2
  • r-tidyr=0.8.1=r351h9d2a408_2
  • r-tidyselect=0.2.4=r351h9d2a408_3
  • r-tidyverse=1.2.1=r351h6115d3f_1001
  • r-tinytex=0.8=r351h6115d3f_1000
  • r-utf8=1.1.4=r351hc070d10_0
  • r-vcd=1.4_4=r351h6115d3f_1001
  • r-viridis=0.5.1=r351h6115d3f_1001
  • r-viridislite=0.3.0=r351h6115d3f_1001
  • r-whisker=0.3_2=r351h6115d3f_1001
  • r-withr=2.1.2=r351h6115d3f_1000
  • r-xfun=0.3=r351h6115d3f_1001
  • r-xml=3.98_1.16=r351hc070d10_0
  • r-xml2=1.2.0=r351h9d2a408_2
  • r-xtable=1.8_3=r351_2000
  • r-yaml=2.2.0=r351hc070d10_1
  • r-zoo=1.8_3=r351hc070d10_0
  • readline=7.0=haf1bffa_1
  • tk=8.6.9=ha92aebf_0
  • xorg-kbproto=1.0.7=h470a237_2
  • xorg-libice=1.0.9=h470a237_4
  • xorg-libsm=1.2.3=h8c8a85c_0
  • xorg-libx11=1.6.6=h470a237_0
  • xorg-libxau=1.0.8=h470a237_6
  • xorg-libxdmcp=1.1.2=h470a237_7
  • xorg-libxext=1.3.3=h470a237_4
  • xorg-libxrender=0.9.10=h470a237_2
  • xorg-libxt=1.1.5=h470a237_2
  • xorg-renderproto=0.11.1=h470a237_2
  • xorg-xextproto=7.3.0=h470a237_2
  • xorg-xproto=7.0.31=h470a237_7
  • xz=5.2.4=h470a237_1
  • zlib=1.2.11=h470a237_3
  • libgcc-ng=7.3.0=hdf63c60_0
  • _r-mutex=1.0.0=anacondar_1
  • blas=1.0=mkl
  • gsl=2.2.1=h0c605f7_3
  • intel-openmp=2019.1=144
  • mkl=2019.1=144
  • wget=1.19.5=h1ad7b7a_0
salmon_quant_alignment 16
  • results/quantification/salmonAlignment/hg38/MK_1-NSQ_1/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_2-NSQsi_1/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_3-HSQ_1/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_4-HSQsi_1/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_5-NSQ_2/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_6-NSQsi_2/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_7-HSQ_2/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_8-HSQsi_2/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_9-NSQ_3/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_10-NSQsi_3/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_11-HSQ_3/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_12-HSQsi_3/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_13-NSQ_4/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_14-NSQsi_4/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_15-HSQ_4/quant.sf
  • results/quantification/salmonAlignment/hg38/MK_16-HSQsi_4/quant.sf
  • salmon=0.12.0
salmon_quant_reads 16
  • results/quantification/salmonReads/hg38/MK_1-NSQ_1/quant.sf
  • results/quantification/salmonReads/hg38/MK_1-NSQ_1/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_2-NSQsi_1/quant.sf
  • results/quantification/salmonReads/hg38/MK_2-NSQsi_1/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_3-HSQ_1/quant.sf
  • results/quantification/salmonReads/hg38/MK_3-HSQ_1/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_4-HSQsi_1/quant.sf
  • results/quantification/salmonReads/hg38/MK_4-HSQsi_1/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_5-NSQ_2/quant.sf
  • results/quantification/salmonReads/hg38/MK_5-NSQ_2/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_6-NSQsi_2/quant.sf
  • results/quantification/salmonReads/hg38/MK_6-NSQsi_2/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_7-HSQ_2/quant.sf
  • results/quantification/salmonReads/hg38/MK_7-HSQ_2/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_8-HSQsi_2/quant.sf
  • results/quantification/salmonReads/hg38/MK_8-HSQsi_2/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_9-NSQ_3/quant.sf
  • results/quantification/salmonReads/hg38/MK_9-NSQ_3/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_10-NSQsi_3/quant.sf
  • results/quantification/salmonReads/hg38/MK_10-NSQsi_3/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_11-HSQ_3/quant.sf
  • results/quantification/salmonReads/hg38/MK_11-HSQ_3/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_12-HSQsi_3/quant.sf
  • results/quantification/salmonReads/hg38/MK_12-HSQsi_3/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_13-NSQ_4/quant.sf
  • results/quantification/salmonReads/hg38/MK_13-NSQ_4/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_14-NSQsi_4/quant.sf
  • results/quantification/salmonReads/hg38/MK_14-NSQsi_4/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_15-HSQ_4/quant.sf
  • results/quantification/salmonReads/hg38/MK_15-HSQ_4/lib_format_counts.json
  • results/quantification/salmonReads/hg38/MK_16-HSQsi_4/quant.sf
  • results/quantification/salmonReads/hg38/MK_16-HSQsi_4/lib_format_counts.json
  • salmon=0.12.0
star 16
  • results/mapping/star/hg38/MK_1-NSQ_1/Aligned.out.bam
  • results/mapping/star/hg38/MK_1-NSQ_1/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_1-NSQ_1/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_2-NSQsi_1/Aligned.out.bam
  • results/mapping/star/hg38/MK_2-NSQsi_1/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_2-NSQsi_1/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_3-HSQ_1/Aligned.out.bam
  • results/mapping/star/hg38/MK_3-HSQ_1/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_3-HSQ_1/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_4-HSQsi_1/Aligned.out.bam
  • results/mapping/star/hg38/MK_4-HSQsi_1/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_4-HSQsi_1/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_5-NSQ_2/Aligned.out.bam
  • results/mapping/star/hg38/MK_5-NSQ_2/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_5-NSQ_2/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_6-NSQsi_2/Aligned.out.bam
  • results/mapping/star/hg38/MK_6-NSQsi_2/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_6-NSQsi_2/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_7-HSQ_2/Aligned.out.bam
  • results/mapping/star/hg38/MK_7-HSQ_2/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_7-HSQ_2/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_8-HSQsi_2/Aligned.out.bam
  • results/mapping/star/hg38/MK_8-HSQsi_2/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_8-HSQsi_2/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_9-NSQ_3/Aligned.out.bam
  • results/mapping/star/hg38/MK_9-NSQ_3/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_9-NSQ_3/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_10-NSQsi_3/Aligned.out.bam
  • results/mapping/star/hg38/MK_10-NSQsi_3/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_10-NSQsi_3/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_11-HSQ_3/Aligned.out.bam
  • results/mapping/star/hg38/MK_11-HSQ_3/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_11-HSQ_3/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_12-HSQsi_3/Aligned.out.bam
  • results/mapping/star/hg38/MK_12-HSQsi_3/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_12-HSQsi_3/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_13-NSQ_4/Aligned.out.bam
  • results/mapping/star/hg38/MK_13-NSQ_4/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_13-NSQ_4/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_14-NSQsi_4/Aligned.out.bam
  • results/mapping/star/hg38/MK_14-NSQsi_4/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_14-NSQsi_4/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_15-HSQ_4/Aligned.out.bam
  • results/mapping/star/hg38/MK_15-HSQ_4/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_15-HSQ_4/Aligned.toTranscriptome.out.bam
  • results/mapping/star/hg38/MK_16-HSQsi_4/Aligned.out.bam
  • results/mapping/star/hg38/MK_16-HSQsi_4/ReadsPerGene.out.tab
  • results/mapping/star/hg38/MK_16-HSQsi_4/Aligned.toTranscriptome.out.bam
  • star=2.6.1b
gzip 32
  • results/trimmed/sickle/MK_1-NSQ_1.1.fastq.gz
  • results/trimmed/sickle/MK_1-NSQ_1.2.fastq.gz
  • results/trimmed/sickle/MK_2-NSQsi_1.1.fastq.gz
  • results/trimmed/sickle/MK_2-NSQsi_1.2.fastq.gz
  • results/trimmed/sickle/MK_3-HSQ_1.1.fastq.gz
  • results/trimmed/sickle/MK_3-HSQ_1.2.fastq.gz
  • results/trimmed/sickle/MK_4-HSQsi_1.1.fastq.gz
  • results/trimmed/sickle/MK_4-HSQsi_1.2.fastq.gz
  • results/trimmed/sickle/MK_5-NSQ_2.1.fastq.gz
  • results/trimmed/sickle/MK_5-NSQ_2.2.fastq.gz
  • results/trimmed/sickle/MK_6-NSQsi_2.1.fastq.gz
  • results/trimmed/sickle/MK_6-NSQsi_2.2.fastq.gz
  • results/trimmed/sickle/MK_7-HSQ_2.1.fastq.gz
  • results/trimmed/sickle/MK_7-HSQ_2.2.fastq.gz
  • results/trimmed/sickle/MK_8-HSQsi_2.1.fastq.gz
  • results/trimmed/sickle/MK_8-HSQsi_2.2.fastq.gz
  • results/trimmed/sickle/MK_9-NSQ_3.1.fastq.gz
  • results/trimmed/sickle/MK_9-NSQ_3.2.fastq.gz
  • results/trimmed/sickle/MK_10-NSQsi_3.1.fastq.gz
  • results/trimmed/sickle/MK_10-NSQsi_3.2.fastq.gz
  • results/trimmed/sickle/MK_11-HSQ_3.1.fastq.gz
  • results/trimmed/sickle/MK_11-HSQ_3.2.fastq.gz
  • results/trimmed/sickle/MK_12-HSQsi_3.1.fastq.gz
  • results/trimmed/sickle/MK_12-HSQsi_3.2.fastq.gz
  • results/trimmed/sickle/MK_13-NSQ_4.1.fastq.gz
  • results/trimmed/sickle/MK_13-NSQ_4.2.fastq.gz
  • results/trimmed/sickle/MK_14-NSQsi_4.1.fastq.gz
  • results/trimmed/sickle/MK_14-NSQsi_4.2.fastq.gz
  • results/trimmed/sickle/MK_15-HSQ_4.1.fastq.gz
  • results/trimmed/sickle/MK_15-HSQ_4.2.fastq.gz
  • results/trimmed/sickle/MK_16-HSQsi_4.1.fastq.gz
  • results/trimmed/sickle/MK_16-HSQsi_4.2.fastq.gz
salmon_index 1
  • references/hg38/salmon_transcriptome_index
  • salmon=0.12.0
sickle_pe 16
  • results/trimmed/sickle/MK_1-NSQ_1.1.fastq
  • results/trimmed/sickle/MK_1-NSQ_1.2.fastq
  • results/trimmed/sickle/MK_1-NSQ_1.output_single.fastq
  • results/trimmed/sickle/TMP---MK_1-NSQ_1.1.fastq
  • results/trimmed/sickle/TMP---MK_1-NSQ_1.2.fastq
  • results/trimmed/sickle/MK_2-NSQsi_1.1.fastq
  • results/trimmed/sickle/MK_2-NSQsi_1.2.fastq
  • results/trimmed/sickle/MK_2-NSQsi_1.output_single.fastq
  • results/trimmed/sickle/TMP---MK_2-NSQsi_1.1.fastq
  • results/trimmed/sickle/TMP---MK_2-NSQsi_1.2.fastq
  • results/trimmed/sickle/MK_3-HSQ_1.1.fastq
  • results/trimmed/sickle/MK_3-HSQ_1.2.fastq
  • results/trimmed/sickle/MK_3-HSQ_1.output_single.fastq
  • results/trimmed/sickle/TMP---MK_3-HSQ_1.1.fastq
  • results/trimmed/sickle/TMP---MK_3-HSQ_1.2.fastq
  • results/trimmed/sickle/MK_4-HSQsi_1.1.fastq
  • results/trimmed/sickle/MK_4-HSQsi_1.2.fastq
  • results/trimmed/sickle/MK_4-HSQsi_1.output_single.fastq
  • results/trimmed/sickle/TMP---MK_4-HSQsi_1.1.fastq
  • results/trimmed/sickle/TMP---MK_4-HSQsi_1.2.fastq
  • results/trimmed/sickle/MK_5-NSQ_2.1.fastq
  • results/trimmed/sickle/MK_5-NSQ_2.2.fastq
  • results/trimmed/sickle/MK_5-NSQ_2.output_single.fastq
  • results/trimmed/sickle/TMP---MK_5-NSQ_2.1.fastq
  • results/trimmed/sickle/TMP---MK_5-NSQ_2.2.fastq
  • results/trimmed/sickle/MK_6-NSQsi_2.1.fastq
  • results/trimmed/sickle/MK_6-NSQsi_2.2.fastq
  • results/trimmed/sickle/MK_6-NSQsi_2.output_single.fastq
  • results/trimmed/sickle/TMP---MK_6-NSQsi_2.1.fastq
  • results/trimmed/sickle/TMP---MK_6-NSQsi_2.2.fastq
  • results/trimmed/sickle/MK_7-HSQ_2.1.fastq
  • results/trimmed/sickle/MK_7-HSQ_2.2.fastq
  • results/trimmed/sickle/MK_7-HSQ_2.output_single.fastq
  • results/trimmed/sickle/TMP---MK_7-HSQ_2.1.fastq
  • results/trimmed/sickle/TMP---MK_7-HSQ_2.2.fastq
  • results/trimmed/sickle/MK_8-HSQsi_2.1.fastq
  • results/trimmed/sickle/MK_8-HSQsi_2.2.fastq
  • results/trimmed/sickle/MK_8-HSQsi_2.output_single.fastq
  • results/trimmed/sickle/TMP---MK_8-HSQsi_2.1.fastq
  • results/trimmed/sickle/TMP---MK_8-HSQsi_2.2.fastq
  • results/trimmed/sickle/MK_9-NSQ_3.1.fastq
  • results/trimmed/sickle/MK_9-NSQ_3.2.fastq
  • results/trimmed/sickle/MK_9-NSQ_3.output_single.fastq
  • results/trimmed/sickle/TMP---MK_9-NSQ_3.1.fastq
  • results/trimmed/sickle/TMP---MK_9-NSQ_3.2.fastq
  • results/trimmed/sickle/MK_10-NSQsi_3.1.fastq
  • results/trimmed/sickle/MK_10-NSQsi_3.2.fastq
  • results/trimmed/sickle/MK_10-NSQsi_3.output_single.fastq
  • results/trimmed/sickle/TMP---MK_10-NSQsi_3.1.fastq
  • results/trimmed/sickle/TMP---MK_10-NSQsi_3.2.fastq
  • results/trimmed/sickle/MK_11-HSQ_3.1.fastq
  • results/trimmed/sickle/MK_11-HSQ_3.2.fastq
  • results/trimmed/sickle/MK_11-HSQ_3.output_single.fastq
  • results/trimmed/sickle/TMP---MK_11-HSQ_3.1.fastq
  • results/trimmed/sickle/TMP---MK_11-HSQ_3.2.fastq
  • results/trimmed/sickle/MK_12-HSQsi_3.1.fastq
  • results/trimmed/sickle/MK_12-HSQsi_3.2.fastq
  • results/trimmed/sickle/MK_12-HSQsi_3.output_single.fastq
  • results/trimmed/sickle/TMP---MK_12-HSQsi_3.1.fastq
  • results/trimmed/sickle/TMP---MK_12-HSQsi_3.2.fastq
  • results/trimmed/sickle/MK_13-NSQ_4.1.fastq
  • results/trimmed/sickle/MK_13-NSQ_4.2.fastq
  • results/trimmed/sickle/MK_13-NSQ_4.output_single.fastq
  • results/trimmed/sickle/TMP---MK_13-NSQ_4.1.fastq
  • results/trimmed/sickle/TMP---MK_13-NSQ_4.2.fastq
  • results/trimmed/sickle/MK_14-NSQsi_4.1.fastq
  • results/trimmed/sickle/MK_14-NSQsi_4.2.fastq
  • results/trimmed/sickle/MK_14-NSQsi_4.output_single.fastq
  • results/trimmed/sickle/TMP---MK_14-NSQsi_4.1.fastq
  • results/trimmed/sickle/TMP---MK_14-NSQsi_4.2.fastq
  • results/trimmed/sickle/MK_15-HSQ_4.1.fastq
  • results/trimmed/sickle/MK_15-HSQ_4.2.fastq
  • results/trimmed/sickle/MK_15-HSQ_4.output_single.fastq
  • results/trimmed/sickle/TMP---MK_15-HSQ_4.1.fastq
  • results/trimmed/sickle/TMP---MK_15-HSQ_4.2.fastq
  • results/trimmed/sickle/MK_16-HSQsi_4.1.fastq
  • results/trimmed/sickle/MK_16-HSQsi_4.2.fastq
  • results/trimmed/sickle/MK_16-HSQsi_4.output_single.fastq
  • results/trimmed/sickle/TMP---MK_16-HSQsi_4.1.fastq
  • results/trimmed/sickle/TMP---MK_16-HSQsi_4.2.fastq
  • sickle-trim=1.33